Semantic Segmentation how to upsampling
You can always train your network with higher resolution images. There is nothing preventing you to do that if you don't have any restriction about inference time. 

Also, the paper is actually mentioning how to upsample. Check for the phrase "Upsample using deconvolutional layers". 

The most common ways to upsample are either using the deconvolutional layer or just by simple resize methods (like image resize).